miga-base 1.3.14.3 → 1.3.14.6

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: ad1cde77838f069107b11a871b01a52062f508aa7770210da8ddec458b8b8064
-  data.tar.gz: 2b15d46aeadfbc73f972c232b0609015e4dcfc72d5aae03bea09f44fe8e8bf5b
+  metadata.gz: 30206d73638543095eec37de708d5994d9dcae5e94cdaf8797d116a74e4c5241
+  data.tar.gz: d88074873e1f52f713bbe39cf8e47f11e946f0d79bd36de0bb12344f4911a617
 SHA512:
-  metadata.gz: 1195c71d940b310670a391d2238020dc4efc954ea4f22ea16ef50083da44e632baed6497064ea16ed22b0870f6e874ddc21be0df5caa4c91556cf62e1b54788b
-  data.tar.gz: 40fba95f7f3dda37a917a08611238e39fdc908153ef33d3e8f9872ccebabe85725bbceb90ca0864f5da32b3c51f16cc04e7f6d3f71a1d6475c97eea323905a4e
+  metadata.gz: e77eba87e956eebd9168c50ba12bb6cb66b6d888887fcac7cb909ce4e9560db0804cca3307d92834da83bfee30974b9df4c58402b8c829a859d9854efc887f5b
+  data.tar.gz: 5cfa6a9e28a745376a44c9abe91478170f51785f813068fbbffd0d29ea48679994d98f56001c0bbc213a5c43f5f8efbb21a6b027c953aed4a94446bc73bc6e73

data/lib/miga/cli/action/run.rb

@@ -84,7 +84,7 @@ class MiGA::Cli::Action::Run < MiGA::Cli::Action
     cmd << MiGA.script_path(cli[:result], miga: miga, project: p).shellescape
     if cli[:remote]
       cmd = [
-        'ssh', '-t', '-t', '-o', 'StrictHostKeyChecking off',
+        'ssh', '-t', '-t', '-o', 'StrictHostKeyChecking off'.shellescape,
         cli[:remote].shellescape,
         cmd.join(' ').shellescape
       ]

data/lib/miga/version.rb

@@ -12,7 +12,7 @@ module MiGA
   # - String indicating release status:
   #   - rc* release candidate, not released as gem
   #   - [0-9]+ stable release, released as gem
-  VERSION = [1.3, 14, 3].freeze
+  VERSION = [1.3, 14, 6].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2024, 4, 13)
+  VERSION_DATE = Date.new(2024, 4, 15)
 
   ##
   # References of MiGA

data/scripts/aai_distances.bash

@@ -40,11 +40,18 @@ rm "miga-project.txt.lno"
 # R-ify
 cat <<R | R --vanilla
 file <- gzfile("miga-project.txt.gz")
-text <- readLines(file, n = $LNO + 1, ok = FALSE)
-list <- strsplit(text[-1], "\t", fixed = TRUE)
-a <- sapply(list, function(x) x[1])
-b <- sapply(list, function(x) x[2])
-d <- sapply(list, function(x) 1 - (as.numeric(x[3]) / 100))
+text <- readLines(file, n = $LNO + 1, ok = FALSE)[-1]
+a <- vector("character", $LNO)
+b <- vector("character", $LNO)
+d <- vector("numeric", $LNO)
+chunk.n <- 1024 * 1024
+for (chunk in seq_len(ceiling(length(text) / chunk.n))) {
+  sel <- (chunk * chunk.n - chunk.n + 1):min(chunk * chunk.n, length(text))
+  list <- strsplit(text[sel], "\t", fixed = TRUE)
+  a[sel] <- sapply(list, function(x) x[1])
+  b[sel] <- sapply(list, function(x) x[2])
+  d[sel] <- sapply(list, function(x) 1 - (as.numeric(x[3]) / 100))
+}
 save(a, b, d, file = "miga-project.rda")
 
 non_self <- a != b

data/scripts/ani_distances.bash

@@ -35,10 +35,17 @@ rm "miga-project.txt.lno"
 cat <<R | R --vanilla
 file <- gzfile("miga-project.txt.gz")
 text <- readLines(file, n = $LNO + 1, ok = FALSE)
-list <- strsplit(text[-1], "\t", fixed = TRUE)
-a <- sapply(list, function(x) x[1])
-b <- sapply(list, function(x) x[2])
-d <- sapply(list, function(x) 1 - (as.numeric(x[3]) / 100))
+a <- vector("character", $LNO)
+b <- vector("character", $LNO)
+d <- vector("numeric", $LNO)
+chunk.n <- 1024 * 1024
+for (chunk in seq_len(ceiling(length(text) / chunk.n))) {
+  sel <- (chunk * chunk.n - chunk.n + 1):min(chunk * chunk.n, length(text))
+  list <- strsplit(text[sel], "\t", fixed = TRUE)
+  a[sel] <- sapply(list, function(x) x[1])
+  b[sel] <- sapply(list, function(x) x[2])
+  d[sel] <- sapply(list, function(x) 1 - (as.numeric(x[3]) / 100))
+}
 save(a, b, d, file = "miga-project.rda")
 
 non_self <- a != b

data/test/remote_dataset_test.rb

@@ -22,10 +22,7 @@ class RemoteDatasetTest < Test::Unit::TestCase
 
   def test_get
     hiv2 = 'M30502.1'
-    # TODO
-    # EMBL Temporarily down, enable back whenever possible!
-    #{ embl: :ebi, nuccore: :ncbi }.each do |db, universe|
-    { nuccore: :ncbi }.each do |db, universe|
+    { embl: :ebi, nuccore: :ncbi }.each do |db, universe|
       rd = MiGA::RemoteDataset.new(hiv2, db, universe)
       assert_equal([hiv2], rd.ids)
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.3.14.3
+  version: 1.3.14.6
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-04-13 00:00:00.000000000 Z
+date: 2024-04-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons